Variant report

Variant	rs9863226
Chromosome Location	chr3:134031942-134031943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134031937-134032574	HCT-116	colon:	n/a	n/a
2	RAD21	chr3:134031829-134032777	HCT-116	colon:	n/a	n/a
3	RAD21	chr3:134031861-134032643	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFIC	chr3:134031923-134032674	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr3:134029943-134032850	ECC-1	luminal epithelium:	n/a	chr3:134031438-134031451 chr3:134030849-134030856 chr3:134031953-134031969 chr3:134032787-134032800
6	CTCF	chr3:134031801-134032509	A549	lung:	n/a	n/a
7	CTCF	chr3:134031840-134031990	NHEK	skin:	n/a	n/a
8	POLR2A	chr3:134031890-134034730	PANC-1	pancreas:	n/a	n/a
9	RAD21	chr3:134031942-134032420	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr3:134031440-134035208	IMR90	lung:	n/a	n/a
11	SP1	chr3:134031872-134033058	A549	lung:	n/a	chr3:134031993-134032002 chr3:134031992-134032001 chr3:134031991-134032003 chr3:134031991-134032003 chr3:134032263-134032274
12	CTCF	chr3:134031920-134032070	HAc	cerebellar:	n/a	n/a
13	CTCF	chr3:134031926-134032269	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
2	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
3	chr3:134027625..134034860-chr3:134199305..134206618,11	MCF-7	breast:
4	chr3:133969328..133972317-chr3:134030794..134032589,3	MCF-7	breast:
5	chr3:134030467..134032307-chr3:134188090..134190697,3	MCF-7	breast:
6	chr3:134031725..134032254-chr3:134069181..134070038,2	MCF-7	breast:
7	chr2:232571662..232573403-chr3:134029904..134032166,2	MCF-7	breast:
8	chr3:134031765..134032298-chr3:134090449..134090996,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240006	TF binding region
ENSG00000187514	Chromatin interaction
ENSG00000260633	Chromatin interaction
ENSG00000214289	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000163785	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1344687	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270733	0.84[ASN][1000 genomes]
rs34426406	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34591691	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34596580	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34688449	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34913236	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35160848	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35369871	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4131649	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4131651	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4234420	0.84[ASN][1000 genomes]
rs4270476	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437113	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4449291	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4470481	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4510358	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4533618	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4558731	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4574266	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682661	0.84[ASN][1000 genomes]
rs4682663	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55721085	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6774600	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71331752	0.81[ASN][1000 genomes]
rs7431754	0.84[ASN][1000 genomes]
rs7614238	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621320	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641605	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7644134	0.81[ASN][1000 genomes]
rs7652144	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289466	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289467	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9866886	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9863226	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs9863226	RP11-375I20.6	cis	Thyroid	GTEx
rs9863226	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs9863226	RP11-375I20.6	cis	Nerve Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134026800-134032400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:134026800-134034800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:134027000-134032200	Enhancers	Fetal Muscle Leg	muscle
5	chr3:134027000-134032400	Enhancers	HSMMtube	muscle
6	chr3:134027000-134032400	Enhancers	NH-A	brain
7	chr3:134027400-134032000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:134027400-134032000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:134027400-134032000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:134027400-134032000	Enhancers	Fetal Intestine Large	intestine
11	chr3:134027400-134032200	Enhancers	Osteobl	bone
12	chr3:134027400-134032400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:134027400-134032400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:134027400-134032400	Enhancers	Brain Substantia Nigra	brain
15	chr3:134027400-134032400	Enhancers	NHDF-Ad	bronchial
16	chr3:134027800-134032200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:134027800-134032400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:134029200-134032400	Enhancers	A549	lung
19	chr3:134029400-134032000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:134029600-134032200	Enhancers	HepG2	liver
21	chr3:134029800-134032400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:134029800-134032400	Enhancers	NHLF	lung
23	chr3:134030000-134032000	Enhancers	Brain Hippocampus Middle	brain
24	chr3:134030000-134032400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:134030000-134032400	Enhancers	Fetal Heart	heart
26	chr3:134030000-134032400	Enhancers	Left Ventricle	heart
27	chr3:134030000-134032400	Enhancers	Lung	lung
28	chr3:134030000-134032600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:134030000-134037200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:134030200-134032000	Enhancers	Pancreas	Pancrea
31	chr3:134030200-134032000	Enhancers	HMEC	breast
32	chr3:134030200-134032600	Weak transcription	Fetal Kidney	kidney
33	chr3:134030200-134034000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:134030400-134032000	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:134030400-134032400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:134030800-134035000	Enhancers	Spleen	Spleen
37	chr3:134031000-134032000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:134031000-134032200	Flanking Active TSS	Liver	Liver
39	chr3:134031000-134032200	Bivalent Enhancer	Fetal Brain Male	brain
40	chr3:134031000-134032400	Enhancers	HUVEC	blood vessel
41	chr3:134031200-134032400	Weak transcription	Gastric	stomach
42	chr3:134031400-134032000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr3:134031400-134032000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:134031400-134032000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:134031400-134032000	Flanking Active TSS	NHEK	skin
46	chr3:134031400-134032200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:134031400-134032200	Weak transcription	Psoas Muscle	Psoas
48	chr3:134031400-134032400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:134031400-134032400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:134031400-134032400	Active TSS	Primary hematopoietic stem cells	blood

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